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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 7399

FusionGeneSummary for CLINT1_UCHL3

check button Fusion gene summary
Fusion gene informationFusion gene name: CLINT1_UCHL3
Fusion gene ID: 7399
HgeneTgene
Gene symbol

CLINT1

UCHL3

Gene ID

9685

7347

Gene nameclathrin interactor 1ubiquitin C-terminal hydrolase L3
SynonymsCLINT|ENTH|EPN4|EPNRUCH-L3
Cytomap

5q33.3

13q22.2

Type of geneprotein-codingprotein-coding
Descriptionclathrin interactor 1clathrin interacting protein localized in the trans-Golgi regionenthoprotinepsin 4epsin-related proteinepsinRubiquitin carboxyl-terminal hydrolase isozyme L3testicular tissue protein Li 221ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)ubiquitin thioesterase L3ubiquitin thiolesterase
Modification date2018052220180523
UniProtAcc

Q14677

P15374

Ensembl transtripts involved in fusion geneENST00000523094, ENST00000530742, 
ENST00000296951, ENST00000411809, 
ENST00000523908, 
ENST00000377595, 
ENST00000606347, 
Fusion gene scores* DoF score3 X 4 X 2=245 X 3 X 5=75
# samples 45
** MAII scorelog2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLINT1 [Title/Abstract] AND UCHL3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneUCHL3

GO:0016579

protein deubiquitination

9521656

TgeneUCHL3

GO:0030163

protein catabolic process

21762696


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVSKCMTCGA-Z2-A8RT-06ACLINT1chr5

157285938

-UCHL3chr13

76134889

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000523094ENST00000377595CLINT1chr5

157285938

-UCHL3chr13

76134889

+
intron-intronENST00000523094ENST00000606347CLINT1chr5

157285938

-UCHL3chr13

76134889

+
intron-3CDSENST00000530742ENST00000377595CLINT1chr5

157285938

-UCHL3chr13

76134889

+
intron-intronENST00000530742ENST00000606347CLINT1chr5

157285938

-UCHL3chr13

76134889

+
5UTR-3CDSENST00000296951ENST00000377595CLINT1chr5

157285938

-UCHL3chr13

76134889

+
5UTR-intronENST00000296951ENST00000606347CLINT1chr5

157285938

-UCHL3chr13

76134889

+
In-frameENST00000411809ENST00000377595CLINT1chr5

157285938

-UCHL3chr13

76134889

+
5CDS-intronENST00000411809ENST00000606347CLINT1chr5

157285938

-UCHL3chr13

76134889

+
In-frameENST00000523908ENST00000377595CLINT1chr5

157285938

-UCHL3chr13

76134889

+
5CDS-intronENST00000523908ENST00000606347CLINT1chr5

157285938

-UCHL3chr13

76134889

+

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FusionProtFeatures for CLINT1_UCHL3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CLINT1

Q14677

UCHL3

P15374

Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). May have a role in transport viaclathrin-coated vesicles from the trans-Golgi network toendosomes. Stimulates clathrin assembly.{ECO:0000269|PubMed:12429846, ECO:0000269|PubMed:12538641}. Deubiquitinating enzyme (DUB) that controls levels ofcellular ubiquitin through processing of ubiquitin precursors andubiquitinated proteins. Thiol protease that recognizes andhydrolyzes a peptide bond at the C-terminal glycine of eitherubiquitin or NEDD8. Has a 10-fold preference for Arg and Lys atposition P3", and exhibits a preference towards 'Lys-48'-linkedubiquitin chains. Deubiquitinates ENAC in apical compartments,thereby regulating apical membrane recycling. Indirectly increasesthe phosphorylation of IGFIR, AKT and FOXO1 and promotes insulin-signaling and insulin-induced adipogenesis. Required for stress-response retinal, skeletal muscle and germ cell maintenance. Maybe involved in working memory. Can hydrolyze UBB(+1), a mutatedform of ubiquitin which is not effectively degraded by theproteasome and is associated with neurogenerative disorders.{ECO:0000269|PubMed:19154770, ECO:0000269|PubMed:21762696,ECO:0000269|PubMed:22689415, ECO:0000269|PubMed:2530630,ECO:0000269|PubMed:9790970}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for CLINT1_UCHL3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_CLINT1_ENST00000411809_chr5_157285938_-_UCHL3_ENST00000377595_chr13_76134889_+_226aa
MLNMWKVRELVDKAFLNNXVYILTGNSLMYMEWILNSLAWYQDQSVQSYFSFLLQKSMKYSEQKRKKKXNLRDKMLHHQYISXSKQSAMP
VEQLDXFMLLQTIKTRCTLNLDQPXKNSWRNLCQXALKNEPDTWRTMMPSELLMRPVPMKVRLRHQVXMRKXIFILLHXFMXMGISMNXM

>In-frame_CLINT1_ENST00000523908_chr5_157285938_-_UCHL3_ENST00000377595_chr13_76134889_+_226aa
MLNMWKVRELVDKAFLNNXVYILTGNSLMYMEWILNSLAWYQDQSVQSYFSFLLQKSMKYSEQKRKKKXNLRDKMLHHQYISXSKQSAMP
VEQLDXFMLLQTIKTRCTLNLDQPXKNSWRNLCQXALKNEPDTWRTMMPSELLMRPVPMKVRLRHQVXMRKXIFILLHXFMXMGISMNXM


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_CLINT1_ENST00000411809_chr5_157285938_-_UCHL3_ENST00000377595_chr13_76134889_+_680nt
ATGTTGAACATGTGGAAGGTGCGCGAGCTGGTGGACAAAGCTTTCTTAAACAATTAGGTCTACATCCTAACTGGCAATTCGTTGATGTAT
ATGGAATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTAT
TCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCT
GTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGG
AATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAG
GTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATG
GGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGC

>In-frame_CLINT1_ENST00000523908_chr5_157285938_-_UCHL3_ENST00000377595_chr13_76134889_+_680nt
ATGTTGAACATGTGGAAGGTGCGCGAGCTGGTGGACAAAGCTTTCTTAAACAATTAGGTCTACATCCTAACTGGCAATTCGTTGATGTAT
ATGGAATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTAT
TCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCT
GTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGG
AATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAG
GTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATG
GGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGC


* Fusion transcript sequences (Full-length transcript).
>In-frame_CLINT1_ENST00000411809_chr5_157285938_-_UCHL3_ENST00000377595_chr13_76134889_+_1006nt
ACTTCCGCTCCACGCAGCGCCTGTGCTGCCGCGTCTCGACGTGTCACCGGCGGCGCCGCTGCTGTGGCAAAGGAAGGAGCTGACTGGGGG
AGTTCGAGGCGGCGGGCGGCGGTGACCCCGGCCTGGAACTGCCCCGGTACGGAAGTGTTCCGGGGTCCGTGGGGAGCAGGAGAGGGAGGC
GGCGGACCGTCCCGCGCGGGGCACGATGTTGAACATGTGGAAGGTGCGCGAGCTGGTGGACAAAGCTTTCTTAAACAATTAGGTCTACAT
CCTAACTGGCAATTCGTTGATGTATATGGAATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTT
CCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTC
ATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGA
TCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTT
ACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTA
GATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATA
GAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAGCTTGTCAATAATGGA
AACACCAAAAACTGTATTATTTGCAACTAAATTTTCTCTGCCATACACTAACTCAAAAATTTTGATATTTTCATTAACTTGATGATTAAA

>In-frame_CLINT1_ENST00000523908_chr5_157285938_-_UCHL3_ENST00000377595_chr13_76134889_+_974nt
GTCTCGACGTGTCACCGGCGGCGCCGCTGCTGTGGCAAAGGAAGGAGCTGACTGGGGGAGTTCGAGGCGGCGGGCGGCGGTGACCCCGGC
CTGGAACTGCCCCGGTACGGAAGTGTTCCGGGGTCCGTGGGGAGCAGGAGAGGGAGGCGGCGGACCGTCCCGCGCGGGGCACGATGTTGA
ACATGTGGAAGGTGCGCGAGCTGGTGGACAAAGCTTTCTTAAACAATTAGGTCTACATCCTAACTGGCAATTCGTTGATGTATATGGAAT
GGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAAC
AGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAAC
AATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGT
GTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGAC
TGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAA
GCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCC
TGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAGCTTGTCAATAATGGAAACACCAAAAACTGTATTATTTGCAACTAAAT


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FusionGenePPI for CLINT1_UCHL3


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
CLINT1GGA2, CLTC, AP1B1, EPS15, DNM1, AP2A1, AP2B1, AP1G1, STAMBPL1, STAMBP, OSBPL10, GABARAPL1, MAP1LC3A, MAP1LC3B, CALM1, ELAVL1, GGA3, CUL3, GGA1, JUN, CLINT1, AP2M1, RPL5, RPS28, RPS6, NFXL1, CFTR, PAN2, CYHR1, RPA3, RPA2, RPA1, AURKB, CDKN1A, CEP250, RNF2, NTRK1, MED4, ODF2, TMEM17, TMEM216, XPO1, CAPZA2, CLTB, DBN1, FLNA, GAK, MYH7, MYH9, NCK1, PPP1CB, RAB5C, DNAJC7, PICALM, DYNLL1, IQGAP1, AP1S2, SEC16A, ATP6AP2, TFG, SYNPO, LIMA1, GTSE1, ANLN, MYO19, MBOAT1, ARX, MYO18A, CDC5L, MYO6, CDH1, PTPN23, CLTCL1, BMP2K, PIK3C2A, SMAP2, STON2, REPS1, LOXL3, RALBP1, VTI1B, STX8, CSTF2T, AP2A2, MAP7D2, VAMP4, RABGEF1, DYNLL2UCHL3NEDD8, COPS5, COPS6, USP20, CLPB, SMAD1, HMP19, POGK, UBC, UBE2S, UCHL3, ATXN7L3, PJA1, TRIM63, TRIM55, TRIM54, USP21, USP15, USP28, TSN, ZFYVE19, AHCYL1, UBA6, ZNF593, USP48, USP9X, SSSCA1, USP34, USP5, UBE2V1, UBQLN1, CSE1L, UBE2A, XIAP, UBXN7, UBR1, UNK, ZYX, SNRPD1, UBE2L3, ZRANB2, ATP6V1F, PCMT1, TTC9C, SULT1A1, YAP1, UBE4B, TTC1, VPS33B, PBX1, NT5DC1, UBL7, LONRF1, TRIM27, BAG3, CDH1, PLA2G2A, ZMYM6, ACAA2, ARHGDIA, GDI1, GPX4, HINT1, IMPDH2, MAPRE1, PEBP1, PGD, STIP1, DLD, ENO1, ENO2, EZR, HSD17B10, ISYNA1, MSN, NUP93, P4HB, PPIB, RDX, SMS, SOD2, SUMO3, TAGLN, TAGLN2, TPD52, TPD52L1, UBA1, RAD51, ATM, ZEB1


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for CLINT1_UCHL3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CLINT1_UCHL3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneUCHL3C0027627Neoplasm Metastasis1CTD_human